Partly due to the thicker string gauge, but also because you will be plucking the string closer to its middle point (if your pick or R.H. finger/thumb plucks in the same place.) This excites fewer of the upper harmonics of the string, giving a mellower sound. In classical guitar music you are often asked to play closer to the middle of the string to produce a mellower sound; this can be marked dolce, which literally translates to sweetly, or can be marked sul tasto (over the fingerboard). The opposite of this is pont. or ponticello (near the bridge) or metallico, which asks for a brittle sound.
On electric guitar this mellow effect, of playing the same note on a lower string, is also due to the relative position of the pickups. Whichever pickup you are using is now closer to the middle of the string. (If you think about the relative positioning, the bridge pickup now has the equivalent positioning of the neck pickup; the neck pickup is now likely to be very close to the middle of the string.)